So one day I was helping a friend with the Hydra and found something interesting. As someone had brought it up earlier in another thread, bringing the Ebon head down the first round caused the glitch in which we couldn't attack him. So we tried again, this time we brought him down on the second round and the battle went on as normal.
So my belief is that there's something in the first round that has caused the glitch and possibly could be the reason why the glitch happens often, since our focus is meant to bring him down and in turn we do it too soon. Maybe more people should test this and wait until the second round to see if the battle goes on as normal?